Evidence map›Paper›PMID 20141761›Full record

ArticleBiophysical journal2010

Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins.

Haipeng Gong, Karl F Freed

Abstract read
In one paragraph

Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Resting and active states of the ERK2:HePTP complex.Journal of the American Chemical Society · 2011
    Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Haipeng GongMOE Key Lab of Bioinformatics, Institute of Bioinformatics and System Biology, School of Life Science, Tsinghua University, Beijing, China. hgong@tsinghua.edu.cn
Karl F Freed

Funding

KINETIC/THERMODYNAMIC/STRUCTURAL STUDIES OF RNA FOLDINGR01GM057880 · NIGMS · UNIVERSITY OF CHICAGO · PI PAN, TAO · 1998 to 2011
$2.6M
Protein Structure Refinement Using a Novel MovesetR01GM081642 · NIGMS · UNIVERSITY OF CHICAGO · PI SOSNICK, TOBIN R · 2007 to 2009
$968k
Kinetic/Thermodynamic/Structural Studies of RNA FoldingR56GM057880 · NIGMS · UNIVERSITY OF CHICAGO · PI PAN, TAO · 2007 to 2007
$307k
NIGMS NIH HHS GM081642NIGMS NIH HHS GM57880NIGMS NIH HHS R01 GM057880NIGMS NIH HHS R01 GM081642NIGMS NIH HHS R56 GM057880
6 · The paper itself

Abstract

Born-type electrostatic continuum methods have been an indispensable ingredient in a variety of implicit-solvent methods that reduce computational effort by orders of magnitude compared to explicit-solvent MD simulations and thus enable treatment using larger systems and/or longer times. An analysis of the limitations and failures of the Born approaches serves as a guide for fundamental improvements without diminishing the importance of prior works. One of the major limitations of the Born theory is the lack of a liquidlike description of the response of solvent dipoles to the electrostatic field of the solute and the changes therein, a feature contained in the continuum Langevin-Debye (LD) model applied here to investigate how Coulombic interactions depend on the location of charges relative to the protein/water boundary. This physically more realistic LD model is applied to study the stability of salt bridges. When compared head to head using the same (independently measurable) physical parameters (radii, dielectric constants, etc.), the LD model is in good agreement with observations, whereas the Born model is grossly in error. Our calculations also suggest that a salt bridge on the protein's surface can be stabilizing when the charge separation is < or =4 A.

Indexed as

Models, ChemicalProtein StabilityStatic ElectricityAlgorithmsComputer SimulationIonsProteinsSaltsWaterIonsProteinsSaltsWater

Identifiers

PMID20141761
PMCPMC2814203

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.